8 Dec 16

1. Introduction

The SVAltAligner walker traverses a set of BAM files to compute alignments to
the alternate alleles of structural variations. This walker is one component
of the SVAltAlign pipeline.

2. Inputs / Arguments

-I <bam-file> : The set of input BAM files containing records to realign.

-altReference <fasta-file> : The fasta file for the alternate allele
reference sequences. The fasta file must be indexed with 'samtools faidx' or
the equivalent. This file should be the output from
GenerateAltAlleleFasta.

-alignMappedReads : If present, then align all reads in the input BAM files,
not just unmapped reads (default false).

-alignUnmappedMates <true/false> : If true (the default), then align
unmapped mates of mapped reads (i.e. reads that have a reference position but
have the unmapped flag set). If set to false, then only reads in the
"unmapped" portion of the BAM file will be aligned.

3. Outputs

-O <bam-file> : The output from this walker is a BAM file containing new
alignments for input reads that align to the alternate allele reference
sequences. If no output file is specified, the output is in SAM format instead
and is written to standard output.